rs850610

chr1-116406090-G-Achr1-116406090-G-Cchr1-116406090-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000369491.2(ATP1A1-AS1):n.345C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 212,480 control chromosomes in the GnomAD database, including 33,788 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.50 (22876 hom., cov: 31)
  • Exomes 𝑓: 0.57 (10912 hom.)
• Consequence: ATP1A1-AS1 ENST00000369491.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655

Genes affected

ATP1A1-AS1 (HGNC:28262): (ATP1A1 antisense RNA 1)

ATP1A1 (HGNC:799): (ATPase Na+/K+ transporting subunit alpha 1) The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of Na+/K+ -ATPases. Na+/K+ -ATPase is an integral membrane protein responsible for establishing and maintaining the electrochemical gradients of Na and K ions across the plasma membrane. These gradients are essential for osmoregulation, for sodium-coupled transport of a variety of organic and inorganic molecules, and for electrical excitability of nerve and muscle. This enzyme is composed of two subunits, a large catalytic subunit (alpha) and a smaller glycoprotein subunit (beta). The catalytic subunit of Na+/K+ -ATPase is encoded by multiple genes. This gene encodes an alpha 1 subunit. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP1A1-AS1	NR_027646.1	n.165-4959C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP1A1-AS1	ENST00000675607.1	n.150-4959C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75350 AN: 151800 Hom.: 22875 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.531

GnomAD4 exome AF: 0.572 AC: 34612 AN: 60562 Hom.: 10912 Cov.: 0 AF XY: 0.580 AC XY: 17806 AN XY: 30706

Gnomad4 AFR exome AF: 0.118

Gnomad4 AMR exome AF: 0.446

Gnomad4 ASJ exome AF: 0.544

Gnomad4 EAS exome AF: 0.255

Gnomad4 SAS exome AF: 0.724

Gnomad4 FIN exome AF: 0.616

Gnomad4 NFE exome AF: 0.673

Gnomad4 OTH exome AF: 0.578

GnomAD4 genome AF: 0.496 AC: 75354 AN: 151918 Hom.: 22876 Cov.: 31 AF XY: 0.495 AC XY: 36728 AN XY: 74240

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.532

Alfa AF: 0.636 Hom.: 46784

Bravo AF: 0.463

Asia WGS AF: 0.469 AC: 1632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.4
Dann	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs850610; hg19: chr1-116948712; COSMIC: COSV55190134;